VCV000018301.2 - ClinVar

NM_000485.3(APRT):c.188-145_296delinsTTCCCGTA

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000485.3(APRT):c.188-145_296delinsTTCCCGTA

Variation ID: 18301 Accession: VCV000018301.2

Type and length

Indel, 254 bp

Location

Cytogenetic: 16q24.3 16: 88810448-88810701 (GRCh38) [ NCBI UCSC ] 16: 88876856-88877109 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Aug 13, 2023	Jan 1, 1997

HGVS

Nucleotide	Protein	Molecular consequence
NM_000485.3:c.188-145_296delinsTTCCCGTA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor
NM_001030018.2:c.188-145_296delinsTTCCCGTA		splice acceptor
NC_000016.10:g.88810448_88810701delinsTACGGGAA
NC_000016.9:g.88876856_88877109delinsTACGGGAA
NG_008013.1:g.6234_6487delinsTTCCCGTA
NG_028266.1:g.11671_11924delinsTACGGGAA

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

OMIM: 102600.0008 VarSome

Comment on variant

NCBI staff provided HGVS expressions for allelic variant 102600.0008 from the sequence reported in Figure 2 of the paper by Menardi et al., 1997 (PubMed 9298830).

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
APRT		-	-	GRCh38 GRCh37	131	250

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Adenine phosphoribosyltransferase deficiency	Pathogenic (1)	no assertion criteria provided	Jan 1, 1997	RCV000019963.28

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jan 01, 1997)	no assertion criteria provided Method: literature only	APRT DEFICIENCY Affected status: not provided Allele origin: germline	OMIM Accession: SCV000040261.2 First in ClinVar: Apr 04, 2013 Last updated: Aug 13, 2023	Publications: PubMed (1) PubMed: 9298830 Comment on evidence: In a Caucasian patient with complete APRT deficiency (614723), Menardi et al. (1997) found compound heterozygosity for 2 mutations in the APRT gene: a common … (more) In a Caucasian patient with complete APRT deficiency (614723), Menardi et al. (1997) found compound heterozygosity for 2 mutations in the APRT gene: a common T insertion at the IVS4 splice donor site (102600.0002) and a novel complex mutation involving simultaneous deletion/insertion and repair events. The second mutation involved a deletion of 254 bp and an insertion of 8 bp exactly at the site of the deletion. Downstream of the mutations, Menardi et al. (1997) found a 14-bp sequence of inverse complementary to this insertion and 6 flanking nucleotides. A more detailed analysis of the region where the deletion had occurred revealed several informative sequence features suitable to explain how the mutation took place. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Human APRT deficiency: indication for multiple origins of the most common Caucasian mutation and detection of a novel type of mutation involving intrastrand-templated repair.	Menardi C	Human mutation	1997	PMID: 9298830

Text-mined citations for this variant ...

Record last updated Aug 13, 2023

ClinVar Genomic variation as it relates to human health

NM_000485.3(APRT):c.188-145_296delinsTTCCCGTA

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...